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Cyclic peptide inhibitor of human PTP1B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HNP PDB ENTRY 2HNP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.72 54.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.69 α = 90 b = 86.82 β = 96.91 c = 52 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 8 78.1 0.029 0.029 13.7 2.9 15934
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 55.7 0.074 0.074 8.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2HNP 2.1 8 15934 997 78.1 0.196 0.262 0.2905 THIN SHELLS 65.49
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 26.4 p_staggered_tor 17.9 p_planar_tor 3.3 p_scangle_it 2.319 p_mcangle_it 2.269 p_scbond_it 1.445 p_mcbond_it 1.408 p_multtor_nbd 0.25 p_singtor_nbd 0.188 p_xyhbond_nbd 0.186
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 26.4 p_staggered_tor 17.9 p_planar_tor 3.3 p_scangle_it 2.319 p_mcangle_it 2.269 p_scbond_it 1.445 p_mcbond_it 1.408 p_multtor_nbd 0.25 p_singtor_nbd 0.188 p_xyhbond_nbd 0.186 p_chiral_restr 0.111 p_angle_d 0.034 p_planar_d 0.031 p_plane_restr 0.0196 p_bond_d 0.01 p_angle_deg p_hb_or_metal_coord p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2495 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction CCP4 data scaling